4
$\begingroup$

I'm looking at some microarray data. For the first time I've calculated a moderated T statistic from limma.

Is there any standard practice for where to cut off that value? For log2 fold change I usually cut off at +/- 1.5 and adjust accordingly; for adjusted p value I cut off at p<0.01 and adjust accordingly.

These moderated T statistics seem a little higher than log2 fold change and I'm not sure what is generally accepted as significant.

Thanks!

Improve this question
$\endgroup$
2
  • 1
    $\begingroup$ If you're filtering by the (adjusted) p-value, why do you want to also filter by moderated T-statistic? The p-value basically comes from the moderated T-statistic, after all. $\endgroup$
    – Devon Ryan
    Oct 19, 2017 at 18:57
  • $\begingroup$ I would like to have values that are real but are also above a particular magnitude. The P value gives me an idea of whether the finding is real, but I also need a way to cut-off on magnitude. I'd usually do this by filtering l|og2Fold|>1.5, but I was hoping to have a similar moderated T-statistic cutoff. Or am I misinterpreting the moderated T statistic? $\endgroup$
    – julianstanley
    Oct 19, 2017 at 19:01

1 Answer 1

Reset to default
3
$\begingroup$

You're misinterpreting the moderated T-statistic, it's basically the fold-change divided by its variance. The p-value comes directly from that, so if you filter by moderated fold-change you're just setting an unknown (unless you go through the trouble of figuring it out) p-value threshold. Instead, do exactly as you've been doing and set appropriate (adjusted) p-value and fold-change thresholds.

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.